#PROG: ALIGNMENT QUALITY METRICS
2D
3D
- no_feature: reads (or read pairs) which could not be assigned to any feature (set S as described above was empty).
- ambiguous: reads (or read pairs) which could have been assigned to more than one feature and hence were not counted for any of these (set S had mroe than one element).
- too_low_aQual: reads (or read pairs) which were skipped due to the -a option.
- not_aligned: reads (or read pairs) in the SAM file without alignment.
- alignment_not_unique: reads (or read pairs) with more than one reported alignment.